Collaborative Proposal: ABI Innovation:A Graph Based Approach for the Genome Wide Prediction of Conditionaly Essential Genes

合作提案：ABI Innovation：基于图形的条件必需基因全基因组预测方法

• 批准号: 1660648
• 负责人: Mark Gerstein
• 金额: $ 120.35万
• 依托单位: Yale University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2022-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1660648&HistoricalAwards=false
• 关键词: Collaborative; Proposal; ABI; Innovation; Graph

How does one identify, and characterize at the genome scale, the set of genes that is essential for an organism to grow and thrive under particular conditions? Predicting such sets of genes is a fundamental goal in bioinformatics; this project aims to create methods and tools for making accurate lists of such functional genes. The approach combines phenotype prediction with knowledge about the functional biological networks in cells to infer new knowledge. The network analysis methods developed here can be easily transferred and applied to a large variety of datasets to answer a wide range of questions from inferring gene-phenotype associations to detecting communities on social networks, extensions highly relevant to the network science community. Moreover, the project's state-of-the-art analysis of temporal gene expression data using state-space models and dimensionality reduction techniques is universally applicable to any groups of genes - e.g. tissue specific vs universally expressed genes. In addition to advancing functional genomics knowledge in the study organism, yeast, the tools will have an impact on research in fields like personal genomics research, by providing a large-scale system-level identification and molecular characterization of phenotypes. Finally, this project provides new and innovative tools for education in bioinformatics. In more technical terms, this project's major goal is to develop new mathematical models and methods that, given a set of genes or an entire genome, can infer their phenotypes and suggest whether or not these genes are necessary for the organism survival. Specifically, information will be integrated on two levels: phenotypic and molecular. At the phenotypic level the structure of biological networks will be used to assign phenotypic attributes to genes and identify sets of genes that share similar essential phenotypes. At the molecular level, the resulted phenotype predictions will be refined by identifying groups of essential genes governed by similar activity patterns. The integration of the information on these two levels will result in a comprehensive gene-phenotype characterization and a refined group of conditionally essential genes. The resulting predictions will be validated experimentally in two yeast systems. All the tools and datasets associated with this project will be made freely available through genopheno.gersteinlab.org.

如何在基因组的尺度上识别和表征生物体在特定条件下生长和繁荣所必需的基因组？预测这样的基因组是生物信息学的一个基本目标;该项目旨在创建方法和工具，以准确列出这些功能基因。该方法将表型预测与细胞中功能生物网络的知识相结合，以推断新的知识。这里开发的网络分析方法可以很容易地转移和应用到各种各样的数据集，以回答广泛的问题，从推断基因-表型关联到检测社交网络上的社区，与网络科学社区高度相关的扩展。此外，该项目使用状态空间模型和降维技术对时间基因表达数据进行的最先进的分析普遍适用于任何基因组-例如组织特异性与普遍表达的基因。除了在研究生物体酵母中推进功能基因组学知识外，这些工具还将通过提供大规模系统级鉴定和表型分子表征，对个人基因组学研究等领域的研究产生影响。最后，该项目为生物信息学教育提供了新的创新工具。用更专业的术语来说，这个项目的主要目标是开发新的数学模型和方法，给定一组基因或整个基因组，可以推断出它们的表型，并表明这些基因是否是生物生存所必需的。具体而言，信息将在两个层面上整合：表型和分子。在表型水平上，生物网络的结构将被用来为基因分配表型属性，并识别具有相似基本表型的基因组。在分子水平上，将通过识别由相似活性模式控制的必需基因组来细化所得到的表型预测。这两个水平上的信息的整合将导致一个全面的基因表型表征和条件必需基因的细化组。由此产生的预测将在两个酵母系统中进行实验验证。与该项目相关的所有工具和数据集将通过genopheno.gersteinlab.org免费提供。

项目成果

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients

• DOI: 10.1186/s13059-020-02033-z
• 发表时间: 2020-06-22
• 期刊: GENOME BIOLOGY
• 影响因子: 12.3
• 作者: Spakowicz, Daniel;Lou, Shaoke;Gerstein, Mark
• 通讯作者: Gerstein, Mark

Cyclic and multilevel causation in evolutionary processes

进化过程中的循环和多层次因果关系

• DOI: 10.1007/s10539-020-09753-3
• 发表时间: 2020
• 期刊: Biology & Philosophy
• 影响因子: 2.5
• 作者: Warrell, Jonathan;Gerstein, Mark
• 通讯作者: Gerstein, Mark

Comparing Technological Development and Biological Evolution from a Network Perspective

从网络角度比较技术发展和生物进化

• DOI: 10.1016/j.cels.2020.02.004
• 发表时间: 2020
• 期刊: Cell Systems
• 影响因子: 9.3
• 作者: Yan, Koon-Kiu;Wang, Daifeng;Xiong, Kun;Gerstein, Mark
• 通讯作者: Gerstein, Mark

Predicting the frequencies of drug side effects

• DOI: 10.1038/s41467-020-18305-y
• 发表时间: 2020-09-11
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Galeano, Diego;Li, Shantao;Paccanaro, Alberto
• 通讯作者: Paccanaro, Alberto